SPAdes – St. Petersburg genome assembler – is intended for both standard isolates and single-cell MDA bacteria assemblies.

• Version: 3.10.1
• Added: September, 2014
• Updated: July, 2017
• Link: http://cab.spbu.ru/software/spades/

See versions of spades which are available:

$ module avail spades

After loading the module, consult the built-in help:

$ spades.py --help

#!/bin/env bash
#SBATCH -p highmem
#SBATCH -n 8
#SBATCH -J spades

module load spades/3.6.1

readonly DATADIR=~/data/bfusca
readonly OUTDIR=/var/scratch/aorth-spades-oct8

# create output directory
mkdir -p ${OUTDIR}

# run spades with 8 CPUs on mammoth (it has 16 logical CPUs, but only 8 are physical)
# run spades with 384 GB of RAM (default is 250, but it ran out of memory before)
spades.py -k 27 -1 ${DATADIR}/1_S1_L001_R1_001_val_1.fastq.gz -2 ${DATADIR}/1_S1_L001_R2_001_val_2.fastq.gz -o ${OUTDIR} -t 8 -m 384

echo
echo "Remember to check (and clean!) output directory on mammoth:"
echo
echo "  ${OUTDIR}"

Notes from the sysadmin during installation:

$ cd /tmp
$ wget  http://cab.spbu.ru/files/release3.11.1/SPAdes-3.11.1.tar.gz
$ tar xf SPAdes-3.11.1.tar.gz
$ cd SPAdes-3.11.1
$ sudo mkdir /export/apps/spades/3.11.1
$ sudo chown aorth /export/apps/spades/3.11.1
$ PREFIX=/export/apps/spades/3.11.1 ./spades_compile.sh
$ sudo chown -R root:root /export/apps/spades/3.11.1

Note: if you get the error Exception caught basic_string::_S_construct null not valid you need to call the spades.py script, not the spades binary!